Speaking as someone who uses Bioconductor due to its extensibility, I cannot agree with the statement posted a couple of weeks ago to the list: "You should not really need to know about the classes -> they should be relatively transparent at the user level. " In order to do anything not written into Bioconductor, I needed to understand the classes. The documentation is good - once I understood what it meant. So, to help others, here are some things I learned. Every object in R has a class. However, some classes are more elementary (e.g. vectors, matrices, tables) and elements are extracted by giving the index (e.g. v[3], or m[1,4]). Many R functions return objects which are lists. Components of a list can be extracted by name (list$mydata) or by component number (list[[3]]). Anything you extract also has a class. Most Bioconductor objects are NOT elementary. The data stored in the Bioconductor objects are extracted by functions which are listed in the documentation. These are called slots. e.g. maRf(myRawMarray) extracts the red foreground from an marrayRaw object). (The ?marrayRaw file was extremely helpful in helping me understand all of this.) Here are some important commands to know: class(myobject) prints the class of your object ?objectclass prints the documentation for the class "objectclass" names(mylist) prints the names of the elements of a list attributes(myobject) gives more information about the object methods(myobject) prints the methods associated with myobject function.class (e.g. plot.ProbeSet is the function that is actually called if you type plot(myprobeset) ) --Naomi Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111